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Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 1 15:55:40 2009 UTC (10 years, 7 months ago) by wilke
Branch: MAIN
CVS Tags: HEAD, mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.43: +2 -2 lines
Diff to previous 1.43
Modified sql query to ? syntax

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 21 05:38:00 2009 UTC (10 years, 9 months ago) by wilke
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.42: +8 -0 lines
Diff to previous 1.42
new method get_organism_name

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 18 17:41:38 2009 UTC (10 years, 9 months ago) by wilke
Branch: MAIN
Changes since 1.41: +60 -11 lines
Diff to previous 1.41
new method get_corresponding_ids

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 13 20:16:31 2009 UTC (10 years, 9 months ago) by wilke
Branch: MAIN
Changes since 1.40: +122 -118 lines
Diff to previous 1.40
stripped version, only db access

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 11 18:05:02 2009 UTC (10 years, 9 months ago) by wilke
Branch: MAIN
Changes since 1.39: +153 -69 lines
Diff to previous 1.39
*** empty log message ***

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 10 17:07:31 2009 UTC (10 years, 9 months ago) by wilke
Branch: MAIN
Changes since 1.38: +4 -0 lines
Diff to previous 1.38
*** empty log message ***

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 3 19:01:47 2009 UTC (10 years, 9 months ago) by wilke
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.37: +21 -5 lines
Diff to previous 1.37
*** empty log message ***

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 14 04:23:35 2009 UTC (10 years, 10 months ago) by wilke
Branch: MAIN
Changes since 1.36: +22 -5 lines
Diff to previous 1.36
changed check for nr directory

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 19 22:39:05 2008 UTC (11 years, 2 months ago) by wilke
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_release_2008_09_29
Changes since 1.35: +39 -7 lines
Diff to previous 1.35
changed names for db tables

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 9 20:53:58 2008 UTC (11 years, 2 months ago) by wilke
Branch: MAIN
CVS Tags: mgrast_rel_2008_0917, mgrast_rel_2008_0919
Changes since 1.34: +156 -16 lines
Diff to previous 1.34
new functions for ACH Resolution

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 30 19:27:27 2008 UTC (11 years, 4 months ago) by wilke
Branch: MAIN
CVS Tags: mgrast_rel_2008_0806, rast_rel_2008_07_21, rast_rel_2008_08_07
Changes since 1.33: +8 -1 lines
Diff to previous 1.33
readonly flag for reading contrib files/indices

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 30 18:48:10 2008 UTC (11 years, 4 months ago) by wilke
Branch: MAIN
Changes since 1.32: +2 -0 lines
Diff to previous 1.32
comment added

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 30 18:33:40 2008 UTC (11 years, 4 months ago) by wilke
Branch: MAIN
Changes since 1.31: +46 -0 lines
Diff to previous 1.31
method to retrieve synonyms for partial ids (prefix)

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 15 20:32:01 2008 UTC (11 years, 5 months ago) by wilke
Branch: MAIN
Changes since 1.30: +333 -4 lines
Diff to previous 1.30
mapping from tigrcmr to cmr

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 12 16:54:42 2008 UTC (11 years, 8 months ago) by paarmann
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.29: +1 -1 lines
Diff to previous 1.29
changed line regexp in clean method

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 11 20:33:59 2008 UTC (11 years, 8 months ago) by paarmann
Branch: MAIN
Changes since 1.28: +82 -26 lines
Diff to previous 1.28
added new index for contrib links (among other things)

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 5 17:35:06 2008 UTC (11 years, 8 months ago) by paarmann
Branch: MAIN
Changes since 1.27: +157 -18 lines
Diff to previous 1.27
added new index for contributed annotations, added new methods

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 8 17:46:19 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.26: +2 -2 lines
Diff to previous 1.26
Fix looping bug when aliases point to themselves.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 4 20:33:11 2008 UTC (11 years, 9 months ago) by paarmann
Branch: MAIN
Changes since 1.25: +14 -10 lines
Diff to previous 1.25
hashing resolved logins to reduce spam

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 4 20:21:26 2008 UTC (11 years, 9 months ago) by paarmann
Branch: MAIN
Changes since 1.24: +25 -3 lines
Diff to previous 1.24
added option to resolve logins to full user names to dump_contrib_annotations

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 13 20:00:18 2007 UTC (11 years, 11 months ago) by paarmann
Branch: MAIN
Changes since 1.23: +65 -0 lines
Diff to previous 1.23
added count and export methods

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 8 18:00:01 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.22: +15 -2 lines
Diff to previous 1.22
fix get_sequence

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 7 16:31:29 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.21: +13 -4 lines
Diff to previous 1.21
ambiguous mapping check on import; fix import bug.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 7 15:42:29 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.20: +1 -1 lines
Diff to previous 1.20
fix alias-tie bug

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 7 15:40:38 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.19: +47 -5 lines
Diff to previous 1.19
multiple id support, build fixes

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 6 22:11:28 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.18: +17 -16 lines
Diff to previous 1.18
Loosen up parsing of tabsep data.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 6 21:44:31 2007 UTC (12 years ago) by olson
Branch: MAIN
Changes since 1.17: +25 -19 lines
Diff to previous 1.17
import_user_annotations now returns in the \@badlist argument a list of the annotations that do not map.
Add aclh command "import" to invoke the import_user_annotations method.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 14 20:14:57 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
doh. fix the method name.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 14 20:01:47 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.15: +27 -0 lines
Diff to previous 1.15
Add get_user suppor to aclh

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 14 15:57:43 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.14: +34 -0 lines
Diff to previous 1.14
Add purge-user-annotations support.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 14 15:41:42 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.13: +2 -0 lines
Diff to previous 1.13
skip blank lines

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 13 19:45:57 2007 UTC (12 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.12: +142 -12 lines
Diff to previous 1.12
Stricter parsing.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 15 18:26:27 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.11: +93 -14 lines
Diff to previous 1.11
New clearinghouse stuff.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 1 21:12:48 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.10: +7 -0 lines
Diff to previous 1.10
fix off-by-one in get_sequence with linelen=0

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 1 20:59:52 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
don't use glimpseserver yet

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 1 20:40:16 2007 UTC (12 years, 3 months ago) by paarmann
Branch: MAIN
Changes since 1.8: +14 -3 lines
Diff to previous 1.8
import_user_annotations takes fh or filename and returns no. of imported annotations

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 1 20:30:22 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.7: +9 -1 lines
Diff to previous 1.7
look for an nr in clearinghouse/<arch> first (intel & ppc formatted nr don't appear to be inter-compatible)

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 1 20:08:08 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.6: +28 -1 lines
Diff to previous 1.6
add more error reporting for fastacmd

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 1 19:58:37 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.5: +10 -3 lines
Diff to previous 1.5
fix up get_sequence()

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 27 18:11:15 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.4: +14 -12 lines
Diff to previous 1.4
fix singletons up

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 25 20:33:49 2007 UTC (12 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.3: +203 -29 lines
Diff to previous 1.3
MOds for latest clearinghouse data formats.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 14 15:31:19 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.2: +8 -0 lines
Diff to previous 1.2
fix for singleton sequences

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 14 14:41:42 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.1: +58 -1 lines
Diff to previous 1.1
more support

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 13 22:11:20 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
perl moduels for annotation clearinghouse

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